[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/pdb PdbAtom.java,1.8,1.9 PdbChain.java,1.9,1.10 PdbGroup.java,1.9,1.10 PdbModel.java,1.5,1.6 PdbPolymer.java,1.7,1.8

[Michael T H. <mic...@us...>]

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb
In directory sc8-pr-cvs1:/tmp/cvs-serv16002/src/org/openscience/jmol/viewer/pdb

Modified Files:
	PdbAtom.java PdbChain.java PdbGroup.java PdbModel.java 
	PdbPolymer.java 
Log Message:
added atom BitSets to PDB objects


Index: PdbAtom.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb/PdbAtom.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- PdbAtom.java	12 Dec 2003 17:52:55 -0000	1.8
+++ PdbAtom.java	15 Dec 2003 22:50:34 -0000	1.9
@@ -140,6 +140,18 @@
     return group.chain.chainID;
   }
 
+  public PdbModel getPdbModel() {
+    return group.chain.model;
+  }
+
+  public PdbChain getPdbChain() {
+    return group.chain;
+  }
+
+  public PdbPolymer getPdbPolymer() {
+    return group.polymer;
+  }
+
   public int getAtomSerial() {
     return atomSerial;
   }

Index: PdbChain.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb/PdbChain.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- PdbChain.java	12 Dec 2003 17:52:55 -0000	1.9
+++ PdbChain.java	15 Dec 2003 22:50:34 -0000	1.10
@@ -26,8 +26,10 @@
 
 import org.openscience.jmol.viewer.*;
 import org.openscience.jmol.viewer.datamodel.Atom;
+import org.openscience.jmol.viewer.datamodel.Frame;
 import java.util.Hashtable;
 import javax.vecmath.Point3f;
+import java.util.BitSet;
 
 public class PdbChain {
 
@@ -37,6 +39,7 @@
   PdbGroup[] groups = new PdbGroup[16];
   PdbGroup[] mainchain;
   PdbPolymer polymer;
+  BitSet atomSet;
 
   public PdbChain(PdbModel model, char chainID) {
     this.model = model;
@@ -49,6 +52,7 @@
       System.arraycopy(groups, 0, t, 0, groupCount);
       groups = t;
     }
+    polymer = new PdbPolymer(this);
   }
   
   PdbGroup allocateGroup(int sequence, String group3) {
@@ -115,8 +119,6 @@
   }
 
   public PdbPolymer getPolymer() {
-    if (polymer == null)
-      polymer = new PdbPolymer(this);
     return polymer;
   }
 
@@ -163,5 +165,19 @@
                          midPoint.x + "," + midPoint.y + "," + midPoint.z);
       */
     }
+  }
+
+  public BitSet getAtomSet() {
+    if (atomSet == null) {
+      BitSet bs = atomSet = new BitSet();
+      Frame frame = model.file.frame;
+      Atom[] atoms = frame.getAtoms();
+      for (int i = frame.getAtomCount(); --i >= 0; ) {
+        Atom atom = atoms[i];
+        if (atom.getPdbChain() == this)
+          bs.set(i);
+      }
+    }
+    return atomSet;
   }
 }

Index: PdbGroup.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb/PdbGroup.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- PdbGroup.java	12 Dec 2003 17:52:55 -0000	1.9
+++ PdbGroup.java	15 Dec 2003 22:50:34 -0000	1.10
@@ -33,6 +33,7 @@
 
   public PdbStructure structure;
   public PdbChain chain;
+  public PdbPolymer polymer;
   public int seqcode;
   public short groupID;
   int[] mainchainIndices;
@@ -41,6 +42,10 @@
     this.chain = chain;
     this.seqcode = seqcode;
     this.groupID = getGroupID(group3);
+  }
+
+  public void setPolymer(PdbPolymer polymer) {
+    this.polymer = polymer;
   }
 
   public void setStructure(PdbStructure structure) {

Index: PdbModel.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb/PdbModel.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- PdbModel.java	12 Dec 2003 17:52:55 -0000	1.5
+++ PdbModel.java	15 Dec 2003 22:50:34 -0000	1.6
@@ -30,11 +30,13 @@
 import javax.vecmath.Point3f;
 import java.util.Hashtable;
 import java.util.Vector;
+import java.util.BitSet;
 
 public class PdbModel {
 
   public PdbFile file;
   public short modelID;
+  BitSet atomSet;
 
   int chainCount = 0;
   PdbChain[] chains = new PdbChain[8];
@@ -95,4 +97,17 @@
     return chains[chainIndex].getMainchain();
   }
 
+  public BitSet getAtomSet() {
+    if (atomSet == null) {
+      BitSet bs = atomSet = new BitSet();
+      Frame frame = file.frame;
+      Atom[] atoms = frame.getAtoms();
+      for (int i = frame.getAtomCount(); --i >= 0; ) {
+        Atom atom = atoms[i];
+        if (atom.getPdbModel() == this)
+          bs.set(i);
+      }
+    }
+    return atomSet;
+  }
 }

Index: PdbPolymer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb/PdbPolymer.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- PdbPolymer.java	12 Dec 2003 17:52:55 -0000	1.7
+++ PdbPolymer.java	15 Dec 2003 22:50:34 -0000	1.8
@@ -26,8 +26,10 @@
 
 import org.openscience.jmol.viewer.*;
 import org.openscience.jmol.viewer.datamodel.Atom;
+import org.openscience.jmol.viewer.datamodel.Frame;
 import java.util.Hashtable;
 import javax.vecmath.Point3f;
+import java.util.BitSet;
 
 public class PdbPolymer {
 
@@ -35,6 +37,7 @@
   int count;
   PdbGroup[] groups;
   int[] atomIndices;
+  BitSet atomSet;
 
   public PdbPolymer(PdbChain chain) {
     this.chain = chain;
@@ -63,6 +66,8 @@
         groups[j++] = group;
       }
     }
+    for (int i = count; --i >= 0; )
+      groups[i].setPolymer(this);
   }
 
   public int getCount() {
@@ -165,5 +170,19 @@
     }
     for (int i = polymerIndexStart; i <= polymerIndexEnd; ++i)
       groups[i].setStructure(structure);
+  }
+
+  public BitSet getAtomSet() {
+    if (atomSet == null) {
+      BitSet bs = atomSet = new BitSet();
+      Frame frame = chain.model.file.frame;
+      Atom[] atoms = frame.getAtoms();
+      for (int i = frame.getAtomCount(); --i >= 0; ) {
+        Atom atom = atoms[i];
+        if (atom.getPdbPolymer() == this)
+          bs.set(i);
+      }
+    }
+    return atomSet;
   }
 }